Moussa Ag Acharatoumane, head of the loyalist Movement for the Safety of Azawad (MSA), said a "climate of terror" prevailed.
"All economic life has come to a halt, the roads have been destroyed," he said.
"(It's) an unprecedented humanitarian crisis," he said, adding that the town of Menaka was being swamped by displaced people.
A mayor in the Menaka administrative region said that in his district, "there's nobody left."
The UN and NGOs have reported repeated attacks against communities accused of abetting the enemy or refusing to join the jihadists.
Hundreds of villagers have died in massacres by ISGS fighters, Human Rights Watch (HRW) said last month.
Eleven were killed on Monday in a raid by gunmen on motorbikes on a camp for displaced people at Kadji, just outside Gao, local officials and humanitarian workers told AFP.
The Islamic State in the Greater Sahara (ISGS) launched an offensive in the Gao and Menaka regions in March, triggering heavy fighting with local armed groups and rival jihadists.
On the Malian side, the army has holed up in the town of Menaka, a tactic that leaves "the way open" for the jihadists, a local elected official who has fled to Bamako told AFP.
"If nothing is done, the whole region will be occupied" by jihadists, a human rights campaigner, contacted by AFP on WhatsApp, said on condition of anonymity.
Witnesses and other sources contacted by AFP confirmed the ISGS' sustained push in this remote and dangerous area, and rights campaigners say civilians have been massacred.
Several sources said that the jihadists had moved into a vacuum left when France pulled its forces out of the region.
The border with neighboring Niger marks the limit of the fighting.
Niger's army is being supported in the air and on the ground by foreign forces, including France's Barkhane mission.
Villages seized by the militants have to pay an Islamic tax and submit to a brutal interpretation of Sharia.
An aid worker in Ansongo said that in the village of Tin-Hama, an unmarried couple aged 50 and 36 were stoned to death in September.
"They dug a hole on weekly market day and placed (them)... in it up to their hips and then threw rocks at them," the source said.
Pro-government forces are trying to muster outside help for their cause, a security source in Niger said.
One idea is to forge an alliance with the former rebels of the Coordination of Azawad Movements (CMA) and Support Group for Islam and Muslims (GSIM), a shadowy group led by an Al-Qaeda-linked Tuareg, Iyad Ag Ghali.
But the chances of creating a joint front are low, an African diplomat in Bamako said.
"Politically, it would seem quite a stretch for people to team up openly with Al-Qaeda today," the diplomat said.